RT Journal Article
SR Electronic
T1 Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
JF Science Translational Medicine
FD American Association for the Advancement of Science
SP 343ra81
OP 343ra81
DO 10.1126/scitranslmed.aad0917
VO 8
IS 343
A1 Yassour, Moran
A1 Vatanen, Tommi
A1 Siljander, Heli
A1 Hämäläinen, Anu-Maaria
A1 Härkönen, Taina
A1 Ryhänen, Samppa J.
A1 Franzosa, Eric A.
A1 Vlamakis, Hera
A1 Huttenhower, Curtis
A1 Gevers, Dirk
A1 Lander, Eric S.
A1 Knip, Mikael
A1 ,
A1 Xavier, Ramnik J.
YR 2016
UL http://stm.sciencemag.org/content/8/343/343ra81.abstract
AB Despite widespread use of antibiotics in children, the effects of antibiotic exposure on the developing infant gut microbiome have remained underexplored. Here, Yassour et al. present a longitudinal study capturing how the gut microbiome responds to and recovers from antibiotic perturbations. Antibiotic-treated children had less stable and less diverse bacterial communities. Antibiotic resistance genes within the guts of these children peaked after antibiotic treatment but generally returned rapidly to baseline. Delivery mode (vaginal versus cesarean) also had strong long-term effects on microbial diversity. These data give insights into the consequences of early life factors such as birth mode and antibiotic treatment on the infant gut microbiome.The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.